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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ), 'gf_id' => 'HOM05D001091', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001091' ), 'data_identifier' => 'HOM05D001091', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001091', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '563', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10540' => 'bna', 'A03p29030' => 'bna', 'A04p27290' => 'bna', 'A04p27300' => 'bna', 'A04p31280' => 'bna', 'A05p01970' => 'bna', 'A05p24520' => 'bna', 'A09p33500' => 'bna', 'A10p18710' => 'bna', 'Aa31LG1G13370' => 'aar', 'Aa31LG3G1110' => 'aar', 'Aa31LG6G7480' => 'aar', 'Aa31LG9G11410' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.713' => 'aag', 'Actinidia04191' => 'ach', 'Actinidia04192' => 'ach', 'Actinidia11652' => 'ach', 'Actinidia23134' => 'ach', 'Actinidia37511' => 'ach', 'Actinidia37764' => 'ach', 'Ah.08g222100' => 'amhyb', 'Ah.12g053330' => 'amhyb', 'Ah.12g059390' => 'amhyb', 'Ah.14g086120' => 'amhyb', 'AL1G46360' => 'aly', 'AL1G47120' => 'aly', 'AL1G58440' => 'aly', 'AL4G38890' => 'aly', 'AL6G32990' => 'aly', 'AL6G44620' => 'aly', 'Aqoxy1G00611' => 'aox', 'Aqoxy1G03632' => 'aox', 'Aqoxy7G00006' => 'aox', 'Aqoxy7G02231' => 'aox', 'Aqoxy7G02725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6F387L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6V7NNJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EB8GYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRDC8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L5AT8N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8EB5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RIT83U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T35U2Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UW76F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1RCBJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZKTD7I' => 'arhy', 'AT1G32850' => 'ath', 'AT2G40930' => 'ath', 'AT4G10570' => 'ath', 'AT4G10590' => 'ath', 'AT5G22030' => 'ath', 'ATR0304G032' => 'atr', 'ATR0585G129' => 'atr', 'ATR0585G135' => 'atr', 'ATR0609G013' => 'atr', 'ATR0697G235' => 'atr', 'Atru.chr1.1293' => 'acertr', 'Atru.chr3.3075' => 'acertr', 'Atru.chr3.3090' => 'acertr', 'Atru.chr8.1306' => 'acertr', 'Atru.chr9.1860' => 'acertr', 'AUR62001573' => 'cqu', 'AUR62002661' => 'cqu', 'AUR62007076' => 'cqu', 'AUR62019940' => 'cqu', 'AUR62020212' => 'cqu', 'AUR62030704' => 'cqu', 'AUR62034029' => 'cqu', 'AUR62036344' => 'cqu', 'BcaB01g01490' => 'bca', 'BcaB01g02746' => 'bca', 'BcaB01g04748' => 'bca', 'BcaB03g13710' => 'bca', 'BcaB05g23890' => 'bca', 'BcaB06g28878' => 'bca', 'BcaB06g28879' => 'bca', 'BcaB08g36457' => 'bca', 'BcaC01g04671' => 'bca', 'BcaC01g06610' => 'bca', 'BcaC02g07664' => 'bca', 'BcaC02g07665' => 'bca', 'BcaC02g12861' => 'bca', 'BcaC04g19537' => 'bca', 'BcaC05g27312' => 'bca', 'BcaC05g27820' => 'bca', 'BcaNung07296' => 'bca', 'BolC2t10259H' => 'bol', 'BolC2t10260H' => 'bol', 'BolC3t13686H' => 'bol', 'BolC3t15820H' => 'bol', 'BolC4t21879H' => 'bol', 'BolC4t27958H' => 'bol', 'BolC4t27959H' => 'bol', 'BolC4t28373H' => 'bol', 'BolC5t31964H' => 'bol', 'BolC5t32548H' => 'bol', 'BolC9t58330H' => 'bol', 'BraA03t10366Z' => 'bra', 'BraA03t12099Z' => 'bra', 'BraA04t18227Z' => 'bra', 'BraA04t18228Z' => 'bra', 'BraA04t18585Z' => 'bra', 'BraA05t21341Z' => 'bra', 'BraA09t38892Z' => 'bra', 'BraA10t43951Z' => 'bra', 'C02p42200' => 'bna', 'C03p12130' => 'bna', 'C03p35090' => 'bna', 'C04p02330' => 'bna', 'C04p64810' => 'bna', 'C04p64820' => 'bna', 'C04p68670' => 'bna', 'C05p32320' => 'bna', 'C05p38200' => 'bna', 'C09p54650' => 'bna', 'CAN.G1463.15' => 'can', 'CAN.G253.7' => 'can', 'CAN.G567.103' => 'can', 'CANSAT21G1175' => 'cansat', 'CANSAT64G0657' => 'cansat', 'CARHR032190' => 'chi', 'CARHR136040' => 'chi', 'CARHR191500' => 'chi', 'CARHR256010' => 'chi', 'Carub.0001s3114' => 'cru', 'Carub.0004s2323' => 'cru', 'Carub.0006s1967' => 'cru', 'Carub.0006s2935' => 'cru', 'Carub.0200s0001' => 'cru', 'Carub.0200s0002' => 'cru', 'Ca_01624_v3' => 'car', 'Ca_08708_v3' => 'car', 'Ca_09067_v3' => 'car', 'Ca_09938_v3' => 'car', 'Ca_09954_v3' => 'car', 'CBR_g19664' => 'cbr', 'CBR_g20064' => 'cbr', 'CBR_g22954' => 'cbr', 'CBR_g26455' => 'cbr', 'Cc01_g07850' => 'ccan', 'Cc01_g15770' => 'ccan', 'Cc06_g06810' => 'ccan', 'Cc08_g16950' => 'ccan', 'CDE02G2806' => 'cde', 'CDE06G2520' => 'cde', 'CDE06G2801' => 'cde', 'CDE08G1529' => 'cde', 'CDE10G0151' => 'cde', 'CDE10G1029' => 'cde', 'CDE11G1199' => 'cde', 'Cfa010206' => 'cfa', 'Cfa011901' => 'cfa', 'Cfa020062' => 'cfa', 'Cfa024859' => 'cfa', 'Cfa025237' => 'cfa', 'Ciclev10012460m.g' => 'ccl', 'Ciclev10013658m.g' => 'ccl', 'Ciclev10013795m.g' => 'ccl', 'Ciclev10024375m.g' => 'ccl', 'Ciclev10027791m.g' => 'ccl', 'CiPaw.01G003800' => 'cil', 'CiPaw.09G022600' => 'cil', 'CiPaw.11G110400' => 'cil', 'CiPaw.12G076100' => 'cil', 'CiPaw.13G126800' => 'cil', 'ClCG01G001440' => 'cla', 'ClCG02G022500' => 'cla', 'ClCG03G002350' => 'cla', 'ClCG10G018140' => 'cla', 'COL.COLO4_00161' => 'col', 'COL.COLO4_07152' => 'col', 'COL.COLO4_10823' => 'col', 'COL.COLO4_29522' => 'col', 'Cpa.g.sc103.29' => 'cpa', 'Cpa.g.sc103.30' => 'cpa', 'Cpa.g.sc103.33' => 'cpa', 'Cpa.g.sc104.6' => 'cpa', 'Cpa.g.sc37.94' => 'cpa', 'Cpa.g.sc92.64' => 'cpa', 'Cre02.g117850' => 'cre', 'CsaV3_1G013030' => 'csa', 'CsaV3_3G038160' => 'csa', 'CsaV3_5G001580' => 'csa', 'CsaV3_6G038640' => 'csa', 'CSS0002029' => 'camsi', 'CSS0006353' => 'camsi', 'CSS0009295' => 'camsi', 'CSS0015567' => 'camsi', 'CSS0017092' => 'camsi', 'CSS0017286' => 'camsi', 'CSS0019153' => 'camsi', 'CSS0022701' => 'camsi', 'CSS0026206' => 'camsi', 'CSS0039255' => 'camsi', 'CSS0046714' => 'camsi', 'CSS0048249' => 'camsi', 'DCAR_006189' => 'dca', 'DCAR_012711' => 'dca', 'DCAR_013447' => 'dca', 'DCAR_013452' => 'dca', 'DCAR_018602' => 'dca', 'DCAR_029901' => 'dca', 'Dinv12892' => 'din', 'Dinv18756' => 'din', 'Dinv18857' => 'din', 'Duzib068G0645' => 'dzi', 'Duzib114G0152' => 'dzi', 'Duzib128G1052' => 'dzi', 'Duzib150G0688' => 'dzi', 'Duzib168G0067' => 'dzi', 'Duzib205G0690' => 'dzi', 'ECA233G5061' => 'eca', 'ECA236G3207' => 'eca', 'ECA238G3615' => 'eca', 'ECA246G0131' => 'eca', 'ECA247G1442' => 'eca', 'ECA247G2982' => 'eca', 'EL10Ac1g01773' => 'bvu', 'EL10Ac5g11835' => 'bvu', 'EL10Ac5g12401' => 'bvu', 'EL10Ac7g16275' => 'bvu', 'Eucgr.A02196' => 'egr', 'Eucgr.A02560' => 'egr', 'Eucgr.D01669' => 'egr', 'Eucgr.J00586' => 'egr', 'FAN02G3563' => 'fan', 'FAN04G0260' => 'fan', 'FAN05G4225' => 'fan', 'FAN05G5163' => 'fan', 'FAN08G3483' => 'fan', 'FAN09G4836' => 'fan', 'FAN11G0955' => 'fan', 'FAN13G1519' => 'fan', 'FAN14G4036' => 'fan', 'FAN16G2369' => 'fan', 'FAN16G2520' => 'fan', 'FAN19G0140' => 'fan', 'FAN21G3893' => 'fan', 'FAN23G0114' => 'fan', 'FAN25G1894' => 'fan', 'FAN26G0026' => 'fan', 'FAN26G0999' => 'fan', 'FAN26G3451' => 'fan', 'FAN28G2885' => 'fan', 'FvH4_1g29170' => 'fve', 'FvH4_3g26140' => 'fve', 'FvH4_5g10610' => 'fve', 'FvH4_6g20680' => 'fve', 'Glyma.03G122400' => 'gma', 'Glyma.03G203700' => 'gma', 'Glyma.10G172400' => 'gma', 'Glyma.12G190400' => 'gma', 'Glyma.13G311300' => 'gma', 'Glyma.19G126500' => 'gma', 'Glyma.19G201100' => 'gma', 'Glyma.20G217800' => 'gma', 'Gohir.A09G101100' => 'ghi', 'Gohir.A09G132900' => 'ghi', 'Gohir.A09G188000' => 'ghi', 'Gohir.A10G193900' => 'ghi', 'Gohir.A12G241400' => 'ghi', 'Gohir.D09G100500' => 'ghi', 'Gohir.D09G129200' => 'ghi', 'Gohir.D09G182800' => 'ghi', 'Gohir.D10G201101' => 'ghi', 'Gohir.D12G242700' => 'ghi', 'Gorai.006G117900' => 'gra', 'Gorai.006G147900' => 'gra', 'Gorai.006G205100' => 'gra', 'Gorai.008G259900' => 'gra', 'Gorai.011G225800' => 'gra', 'GSVIVG01001899001' => 'vvi', 'GSVIVG01019677001' => 'vvi', 'GSVIVG01022581001' => 'vvi', 'GSVIVG01022582001' => 'vvi', 'GSVIVG01037531001' => 'vvi', 'HanXRQChr01g0010511' => 'han', 'HanXRQChr02g0053321' => 'han', 'HanXRQChr06g0166701' => 'han', 'HanXRQChr08g0231261' => 'han', 'HanXRQChr13g0398631' => 'han', 'HanXRQChr13g0398641' => 'han', 'HanXRQChr17g0534101' => 'han', 'HanXRQChr17g0561191' => 'han', 'Haze_09197' => 'cav', 'Haze_20136' => 'cav', 'Haze_20268' => 'cav', 'Haze_20269' => 'cav', 'Haze_23594' => 'cav', 'Haze_26689' => 'cav', 'Hma1.2p1_0101F.1_g049670' => 'hma', 'Hma1.2p1_0161F.1_g071810' => 'hma', 'Hma1.2p1_0198F.1_g085200' => 'hma', 'Hma1.2p1_0456F.1_g156813' => 'hma', 'Hma1.2p1_1223F.1_g268370' => 'hma', 'Hma1.2p1_1514F.1_g288150' => 'hma', 'Hma1.2p1_2082F.1_g313560' => 'hma', 'HPP92_014597' => 'vpl', 'HPP92_028256' => 'vpl', 'Hund10841' => 'sun', 'Hund11338' => 'sun', 'Hund17702' => 'sun', 'Hund18804' => 'sun', 'Lalb_Chr01g0005811' => 'lal', 'Lalb_Chr01g0017791' => 'lal', 'Lalb_Chr02g0149551' => 'lal', 'Lalb_Chr03g0028511' => 'lal', 'Lalb_Chr03g0028521' => 'lal', 'Lalb_Chr06g0168601' => 'lal', 'Lalb_Chr19g0136151' => 'lal', 'Lalb_Chr20g0111281' => 'lal', 'Lalb_Chr21g0311531' => 'lal', 'Lalb_Chr21g0311541' => 'lal', 'Lalb_Chr21g0311551' => 'lal', 'Lalb_Chr21g0311561' => 'lal', 'Lalb_Chr21g0311571' => 'lal', 'Lalb_Chr22g0357871' => 'lal', 'Lalb_Chr25g0287901' => 'lal', 'Lj1C1058G17' => 'lonja', 'Lj1C107G3' => 'lonja', 'Lj1g0000533' => 'lja', 'Lj1g0016178' => 'lja', 'Lj2C154G3' => 'lonja', 'Lj2C949G1' => 'lonja', 'Lj3g0006295' => 'lja', 'Lj5g0007851' => 'lja', 'Lsat_1_v5_gn_2_35221' => 'lsa', 'Lsat_1_v5_gn_3_14860' => 'lsa', 'Lsat_1_v5_gn_5_60300' => 'lsa', 'Lsat_1_v5_gn_6_34761' => 'lsa', 'Lsat_1_v5_gn_7_115660' => 'lsa', 'Lsat_1_v5_gn_8_98701' => 'lsa', 'Lsat_1_v5_gn_9_15821' => 'lsa', 'Manes.01G056100' => 'mes', 'Manes.02G001100' => 'mes', 'Manes.06G031201' => 'mes', 'Manes.09G043300' => 'mes', 'Manes.11G103600' => 'mes', 'Mapoly0003s0311' => 'mpo', 'Mapoly0004s0252' => 'mpo', 'MBI04_g22058_MAGBIO' => 'mbi', 'MBI04_g22059_MAGBIO' => 'mbi', 'MBI05_g36783_MAGBIO' => 'mbi', 'MBI05_g45097_MAGBIO' => 'mbi', 'MCO01G654' => 'mco', 'MD00G1072700' => 'mdo', 'MD03G1159600' => 'mdo', 'MD06G1121900' => 'mdo', 'MD11G1174900' => 'mdo', 'MD12G1043100' => 'mdo', 'MD14G1042200' => 'mdo', 'MD14G1138300' => 'mdo', 'MD17G1207100' => 'mdo', 'Medtr1g077980' => 'mtr', 'Medtr2g087710' => 'mtr', 'Medtr7g088760' => 'mtr', 'Medtr7g106570' => 'mtr', 'MELO3C005015.2' => 'cme', 'MELO3C005793.2' => 'cme', 'MELO3C009559.2' => 'cme', 'MELO3C014526.2' => 'cme', 'Migut.D02381' => 'egut', 'Migut.E00726' => 'egut', 'Migut.J00745' => 'egut', 'Migut.N00688' => 'egut', 'MSTRG.12205' => 'ama', 'MSTRG.17949' => 'ama', 'MSTRG.18797' => 'ama', 'MSTRG.19332' => 'ama', 'MSTRG.21007' => 'ama', 'MSTRG.24869' => 'ama', 'Nitab4.5_0000875g0120' => 'nta', 'Nitab4.5_0001015g0060' => 'nta', 'Nitab4.5_0002520g0110' => 'nta', 'Nitab4.5_0003419g0100' => 'nta', 'Nitab4.5_0003657g0030' => 'nta', 'Nitab4.5_0010253g0020' => 'nta', 'Nn1g00432' => 'nnu', 'Nn1g07098' => 'nnu', 'Nn3g18864' => 'nnu', 'Nn6g34617' => 'nnu', 'Oeu015750.1' => 'oeu', 'Oeu020441.2' => 'oeu', 'Oeu030357.1' => 'oeu', 'Oeu042853.1' => 'oeu', 'Oeu042854.1' => 'oeu', 'Oeu048823.1' => 'oeu', 'Oeu058122.3' => 'oeu', 'Oeu058192.1' => 'oeu', 'Os07g0160000' => 'osa', 'Os10g0160000' => 'osa', 'Os11g0473200' => 'osa', 'Os11g0473350' => 'osa', 'Os11g0667400' => 'osa', 'Os12g0621000' => 'osa', 'Peaxi162Scf00074g00138' => 'pax', 'Peaxi162Scf00098g00113' => 'pax', 'Peaxi162Scf00424g00813' => 'pax', 'PGR004G1296' => 'pgr', 'PGR031G0051' => 'pgr', 'PGR042G2897' => 'pgr', 'PGR119G1581' => 'pgr', 'PGSC0003DMG400012226' => 'stu', 'PGSC0003DMG400020291' => 'stu', 'Phvul.001G118800' => 'pvu', 'Phvul.001G197200' => 'pvu', 'Phvul.005G117700' => 'pvu', 'Phvul.L004601' => 'pvu', 'Potri.001G214800' => 'ptr', 'Potri.001G449000' => 'ptr', 'Potri.006G033800' => 'ptr', 'Potri.006G201100' => 'ptr', 'Potri.011G152500' => 'ptr', 'Potri.016G031900' => 'ptr', 'Potri.016G067400' => 'ptr', 'PRCOL_00002136' => 'pco', 'PRCOL_00006111' => 'pco', 'Prupe.5G132600' => 'ppe', 'Prupe.6G147300' => 'ppe', 'Prupe.7G027000' => 'ppe', 'Prupe.7G027100' => 'ppe', 'Prupe.7G091700' => 'ppe', 'Psat0s1824g0120' => 'psa', 'Psat1g125520' => 'psa', 'Psat1g221360' => 'psa', 'Psat3g027680' => 'psa', 'Psat3g027720' => 'psa', 'Psat3g027760' => 'psa', 'Psat3g081680' => 'psa', 'Psat5g262560' => 'psa', 'Psat6g052920' => 'psa', 'Psat6g052960' => 'psa', 'Psat6g105680' => 'psa', 'Psat7g153840' => 'psa', 'PSO063G1798' => 'pso', 'PSO210G5535' => 'pso', 'PSO339G5290' => 'pso', 'PSO384G3742' => 'pso', 'PSO782G3112' => 'pso', 'PSO832G0993' => 'pso', 'QL01p019200' => 'qlo', 'QL01p019208' => 'qlo', 'QL02p027422' => 'qlo', 'QL07p013120' => 'qlo', 'QL07p027131' => 'qlo', 'RcHm_v2.0_Chr2g0154131' => 'rch', 'RcHm_v2.0_Chr3g0455291' => 'rch', 'RcHm_v2.0_Chr3g0476581' => 'rch', 'RcHm_v2.0_Chr3g0478841' => 'rch', 'RcHm_v2.0_Chr3g0494551' => 'rch', 'RcHm_v2.0_Chr5g0049121' => 'rch', 'RcHm_v2.0_Chr7g0187531' => 'rch', 'Rhsim03G0059600' => 'rsi', 'Rhsim07G0076400' => 'rsi', 'Rhsim13G0055800' => 'rsi', 'Rhsim13G0198100' => 'rsi', 'Sabra06G0022400' => 'sbr', 'Sabra06G0154800' => 'sbr', 'Sabra11G0148300' => 'sbr', 'Sabra12G0075000' => 'sbr', 'Sabra16G0035100' => 'sbr', 'Sabra16G0128400' => 'sbr', 'SalBow1G7663' => 'sbo', 'SalBow2G0137' => 'sbo', 'SalBow6G2252' => 'sbo', 'SalBow6G2883' => 'sbo', 'SalBow6G7235' => 'sbo', 'Sc01g0010810' => 'sci', 'Sc07g0006330' => 'sci', 'Sc07g0006340' => 'sci', 'Sc17g0004620' => 'sci', 'Sc21g0006730' => 'sci', 'Sed0004228' => 'sed', 'Sed0006075' => 'sed', 'Sed0014395' => 'sed', 'Sed0022355' => 'sed', 'Sed0024629' => 'sed', 'Sed0027161' => 'sed', 'SEGI_01669' => 'sgi', 'SEGI_07936' => 'sgi', 'SEGI_08854' => 'sgi', 'SEGI_29448' => 'sgi', 'SGA_v2.0_scaffold104G30251' => 'sas', 'SGA_v2.0_scaffold112G31680' => 'sas', 'SGA_v2.0_scaffold31G12812' => 'sas', 'SGA_v2.0_scaffold36G14269' => 'sas', 'SGA_v2.0_scaffold56G19958' => 'sas', 'SGA_v2.0_scaffold77G25324' => 'sas', 'SGA_v2.0_scaffold7G04006' => 'sas', 'SHI24549' => 'shi', 'SHI24551' => 'shi', 'SHI25267' => 'shi', 'SHI53473' => 'shi', 'SMO119G0162' => 'smo', 'SMO119G0183' => 'smo', 'SMO203G0253' => 'smo', 'SMO338G0040' => 'smo', 'SMO356G0318' => 'smo', 'SMO358G0288' => 'smo', 'SMO364G0888' => 'smo', 'Solyc06g073930.4' => 'sly', 'Solyc08g083300.4' => 'sly', 'Solyc09g019970.3' => 'sly', 'Sopen06g030330' => 'spe', 'Sopen08g031510' => 'spe', 'Sopen09g012740' => 'spe', 'Sp1g28150' => 'spa', 'Sp4g23240' => 'spa', 'Sp6g06860' => 'spa', 'Sp6g23160' => 'spa', 'TAR624G1242' => 'tar', 'TAR626G0838' => 'tar', 'TAR629G2137' => 'tar', 'TAR633G1177' => 'tar', 'TAR636G1107' => 'tar', 'TAR636G1693' => 'tar', 'TAR636G1835' => 'tar', 'THA.LOC104799571' => 'tha', 'THA.LOC104803230' => 'tha', 'THA.LOC104810942' => 'tha', 'THA.LOC104813064' => 'tha', 'THA.LOC104815366' => 'tha', 'Thecc.03G218100' => 'tca', 'Thecc.05G108000' => 'tca', 'Thecc.09G267800' => 'tca', 'Thecc.10G130300' => 'tca', 'Thhalv10006750m.g' => 'esa', 'Thhalv10012650m.g' => 'esa', 'Thhalv10016401m.g' => 'esa', 'Thhalv10027354m.g' => 'esa', 'Thhalv10028406m.g' => 'esa', 'TPR.G17172' => 'tpr', 'TPR.G17437' => 'tpr', 'TPR.G21598' => 'tpr', 'TPR.G25811' => 'tpr', 'TPR.G4164' => 'tpr', 'TWI15G0774' => 'twi', 'TWI31G0595' => 'twi', 'TWI74G0943' => 'twi', 'TWI77G0388' => 'twi', 'TWI79G0355' => 'twi', 'unitig_0.g1155' => 'ugi', 'unitig_22.g5633' => 'ugi', 'unitig_8.g3580' => 'ugi', 'unitig_8.g3581' => 'ugi', 'unitig_899.g15383' => 'ugi', 'unitig_899.g15384' => 'ugi', 'vmacro02847' => 'vma', 'vmacro04051' => 'vma', 'vmacro07506' => 'vma', 'vmacro07507' => 'vma', 'vmacro07865' => 'vma', 'vmacro11493' => 'vma', 'vmacro13839' => 'vma', 'vmacro22680' => 'vma', 'VMungo0720G2397' => 'vmu', 'VMungo1080G0672' => 'vmu', 'VMungo1383G0555' => 'vmu', 'VMungo1383G3391' => 'vmu', 'Zm00001eb026810' => 'zma', 'Zm00001eb090590' => 'zma', 'Zm00001eb134530' => 'zma', 'Zm00001eb300350' => 'zma' ) $gf_id = 'HOM05D001091' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001091' ) $data_identifier = 'HOM05D001091' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 17, 'bol' => (int) 11, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 6, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 19, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 7, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 15, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 5, 'psa' => (int) 12, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb300350' $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